Hi,
Have you specified the right form factor for Se given
the wavelength used in your experiment?
anomalous formfactor [Name] [f'] [f'']
You can also try the new option where you can do simultaneous
SAD phasing and refinement. See: http://tinyurl.com/8on2cr
You will have to upgrade from your present REFMAC5.2 version to use
these functions.
Best regards,
Martin
On Dec 20, 2008, at 5:17 AM, Dima Klenchin wrote:
> Hello,
>
> I am at a loss on what's going on:
>
> I am refining SeMET containing structure and using REFMAC 5.2.0005
> on Linux and, the same thing happening, using REFMAC 5.5.0070 on
> Windows.
>
> When MET were modelled, there were no difference peaks anywhere.
> When I changed them all to MSE, the large difference density peaks
> showed up. So either the protein does not contain SeMet or Refmac
> somehow uses sulfur scattering factors during refinement.
>
> I have hard time believing the former because 1) the protein was
> checked by mass spec to be correct size for SeMet derivative, 2) the
> structure was solved by SAD with all five sites correctly found (196
> residues total), 3) first 50 aa of the protein are identical to a
> known structure.
>
> This is 2.4A resolution and at this point R/Rfree = 25/29.
>
> Refmac log shows correct scattering factors read out:
> SE 17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543
> 43.8163 2.8409
>
> The PDB has this for MSE:
> ATOM 1140 N MSE A 143 35.708 161.163 13.715 1.00
> 78.82 N
> ATOM 1141 CA MSE A 143 35.995 162.467 13.106 1.00
> 77.86 C
> ATOM 1142 CB MSE A 143 36.307 162.307 11.617 1.00
> 78.79 C
> ATOM 1143 CG MSE A 143 37.755 162.127 11.119 1.00
> 80.89 C
> ATOM 1144 SE MSE A 143 37.503 161.104 9.363 1.00
> 91.22 SE
> ATOM 1145 CE MSE A 143 39.169 160.021 9.696 1.00
> 86.47 C
> ATOM 1146 C MSE A 143 34.709 163.226 13.030 1.00
> 77.70 C
> ATOM 1147 O MSE A 143 34.682 164.436 12.737 1.00
> 77.33 O
>
> Any clues greatly appreciated!
>
> Dima
>
>
>
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